Rfam 11.0: 10 years of RNA families

Abstract

The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.

Figure 1.

Growth of Rfam families and sequence regions annotated per each Rfam release. Dates are in MM/YY format.

Figure 2.

(a) Rfam types organized according to their coverage of sequence space. Size of rectangles is proportional to the number of regions annotated by families of that Rfam type; colour of rectangles is proportional to the number of families of that type. (b) Taxonomic coverage of Rfam families. Families have been categorized according to the taxonomic groups covered by the seed sequences, and families in clans are treated as belonging to a single family. This analysis omits six families where the seed contains only unclassified sequences.

Figure 3.

Sunburst visualization of family taxonomy for RF01051, the cyclic di-GMP-I riboswitch. Users may select regions of taxonomic space and use the controls on the left to download an alignment of their chosen subset of species.